Ultrastructure of fibroin in the silk gland of larval Bombyx mori

The fibroin molecules stored in Golgi vacuoles in the posterior silk gland cells of 72-h-old, fifth instar larvae of Bombyx mori L. were observed electron-microscopically. The fibers which float in the Golgi vacuoles often have their ends attached to the limiting membrane. The fibers are helical bundles about 130 Å in diameter composed of 5–7 threads, each 20–30 Å thick.     

Inhibition of the progesterone-dependent induction of meiosis by gammexane in Xenopus laevis oocytes.

Bundles of fibers of hemoglobin S in the presence of 2,3-diphosphoglycerate or inositol hexaphosphate have been prepared from stirred solutions and examined by electron microscopy. The bundles are found to contain ordered arrays of fibers in an eight-stranded form, with strands staggered by 37 Å, as characterized by optical and computer transforms. The characteristic reflections observed for individual fibers are also seen for large areas of the bundles, indicating the presence of the same form of the fibers throughout the bundles. Since 2,3-diphosphoglycerate is the natural hemoglobin cofactor, the structure observed in these studies is likely to bear a close correspondence to the structure $\text{in vivo}$.     

Iodination-Coupled Tetrazonium and Ferric Ferricya-Nide Reduction Stains for Differentiating Red Blood Cells Containing Fetal or Adult Hemoglobin

Either the iodination-coupled tetrazonium reaction or the ferric ferricyanide reduction procedure can be used to differentiate red blood cells containing fetal hemoglobin (hemoglobin F) from those containing adult hemoglobin (hemoglobin A) in blood smears. Oxalated blood is diluted with 3 parts of physiological saline, and smears are made on slides. The air-dried slides are treated with absolute ethanol for 2 min, dried, and placed in phosphate-citrate buffer of pH 3.2-3.6 for 1 min at 37°C. They are then rinsed in distilled water, and dried for storage or stained at once by either the iodination-coupled tetrazonium or the ferric ferricyanide reduction procedure. Adult hemoglobin is extracted by the buffer, so that red blood cells containing fetal hemoglobin give a much darker stain than those containing adult hemoglobin. The hemoglobin S of patients with sickle-cell anemia behaves like adult hemoglobin.     

The cytoplasmic filament system in critical point-dried whole mounts and plastic-embedded sections

High voltage electron microscopy of intact cells prepared by the critical point drying (CPD) procedure has become an important tool in the study of three-dimensional relationships between cytoplasmic organelles. It has been claimed that critical point-dried specimens reveal a structure that is not visible in sections of plastic-embedded material; it has also been claimed that this structure, in association with known cytoplasmic filaments, forms a meshwork of tapering threads ("microtrabecular lattice"). Alternatively, this structure might be a surface tension artifact produced during CPD. To test possible sources of artifacts during CPD, model fiber systems of known structure were used. It was found that traces of water or ethanol in the CO2 caused distortions and fusion of fibers in pure muscle actin, fibrin, collagen, chromatin, and microtubules that produce a structure very similar to the proposed "microtrabecular lattice." These structures were, however, well preserved if water and ethanol were totally excluded from the CO2. The same results were obtained with whole mounts of cultured cells. A "microtrabecular lattice" was obtained if some water or ethanol was present in the pressure chamber. On the other hand, when water or ethanol were totally excluded from the CO2 during CPD, cytoplasmic filaments were uniform in thickness similar to their appearance in sections of plastic-embedded cells. It is concluded that the "microtrabecular lattice" is a distorted image of the cytoplasmic filament network produced during CPD by traces of water or ethanol in the CO2.     

Effect of poly(ADP-ribosyl)ation and Mg2+ ions on chromatin structure revealed by scanning force microscopy

Poly(ADP-ribosyl)ation of nuclear proteins is responsible for major changes in the high-order chromatin structure. The effects of this post-translation modification on nuclear architecture were examined at different Mg2+ concentrations using scanning force microscopy. A quantitative analysis of the internucleosomal distance, the width, and the volume of chromatin fibers imaged in tapping mode reveals that poly(ADP-ribosyl)ation induces a complete relaxation and decondensation of the chromatin structure. Our data, on the center-to-center distance between adjacent nucleosomes and on the fiber width, indicate that the poly(ADP-ribosyl)ated fibers remain significantly decondensed even in the presence of Mg2+. Our results also show that the Mg2+ assumes an important role in the folding of chromatin structure, but Mg2+ is not able to restore the native feature of chromatin, when the fibers are depleted of H1/H5 histones. The combined effect of post-translation modification and cation ions on the chromatin structure shows that poly(ADP-ribosyl)ation could promote accessibility to DNA even in those nuclear processes that require Mg2+.     

Relationship between relative dry mass and average band width in regions of polytene chromosomes of Drosophila

Whole-mounted polytene chromosomes from Drosophila melanogaster were prepared for high-voltage electron microscopy. Relative dry mass of chromosome regions was estimated by densitometry of electron microscopic negatives. Comparison of dry mass of regions of the male X chromosome with that of regions of associated autosomes established that dry mass values are proportional to DNA content. Relative dry mass values of regions of polytene chromosomes from salivary glands, fat body, and malpighian tubules were correlated with the average diameter of bands in these regions: as mass doubled, band width increased by a factor of approximately 2. To provide a standard for estimating absolute levels of polyteny, band widths were measured for chromosomes representing one major polytene class, 256n. These chromosomes were observed to have an average band width of 0.9 m — These observations provide limits to models of chromatin organization in bands. For each chromatid, this area can accommodate up to five chromatin fibers of 250 Å diameter. This value may represent the extent of folding of a chromatin fiber in an average band. Alternatively, a chromatin fiber of higher-order structure could have a maximum diameter of 560 Å in an average band.     

Studies on the Mitotic Prophase Chromosomal Fibers in Vicia faba

The observations have been made on the structures of mitotic prophase nuclei and chromosomes in Vicia faba root meristematic cells. Two methods, i.e., the cell squashing and the nucleus isolation methods, were applied in present study to prepare the specimen of chromosomes and nuclei. Chromosomal fibers 0.3—0.5 μm in diameter were observed in the squashed preparations stained with Giemsa, and in the isolated nucleus preparations treated with 0.05% EDTA followed by Giemsa staining. Using Feulgen reaction, it has been demonstrated that these fibers are nuclear origin containing DNA. The results suggest that this order of chromosomal fiber may be one structural level in the chromosomes in Vicia faba. This conclusion is in support of the view which holds that there exists an intermediate level of structure between the 250–300Å chromatin fiber and the chromosome.     

An Insight into the pathway of the amyloid fibril formation of hen egg white lysozyme obtained from a small-angle X-ray and neutron scattering study

It is known that hen egg white lysozyme (HEWL) forms amyloid fibrils. Since HEWL is one of the proteins that have been studied most extensively and is closely related to human lysozyme, the variants of which form the amyloid fibrils that are related to hereditary systemic amyloidosis, this protein is an ideal model to study the mechanism of amyloid fibril formation. In order to gain an insight into the mechanism of amyloid fibril formation, systematic and detailed studies to detect and characterize various structural states of HEWL were conducted. Since HEWL forms amyloid fibrils in highly concentrated ethanol solutions, solutions of various concentrations of HEWL in various concentrations of ethanol were prepared, and the structures of HEWL in these solutions were investigated by small-angle X-ray and neutron scattering. It was shown that the structural states of HEWL were distinguished as the monomer state, the state of the dimer formation, the state of the protofilament formation, the protofilament state, and the state towards the formation of amyloid fibrils. A phase diagram of these structural states was obtained as a function of protein, water and ethanol concentrations. It was found that under the monomer state the structural changes of HEWL were not gross changes in shape but local conformational changes, and the dimers, formed by the association at the end of the long axis of HEWL, had an elongated shape. Circular dichroism measurements showed that the large changes in the secondary structures of HEWL occurred during dimer formation. The protofilaments were formed by stacking of the dimers with their long axis (nearly) perpendicular to and rotated around the protofilament axis to form a helical structure. These protofilaments were characterized by their radius of gyration of the cross-section of 2.4nm and the mass per unit length of 16,000(+/-2300)Da/nm. It was shown that the changes of the structural states towards the amyloid fibril formation occurred via lateral association of the protofilaments. A pathway of the amyloid fibril formation of HEWL was proposed from these results.     

Chromatin fiber breaks into clutches under tension and crowding

The arrangement of nucleosomes inside chromatin is of extensive interest. While in vitro experiments have revealed the formation of 30 nm fibers, most in vivo studies have failed to confirm their presence in cell nuclei. To reconcile the diverging experimental findings, we characterized chromatin organization using a residue-level coarse-grained model. The computed force–extension curve matches well with measurements from single-molecule experiments. Notably, we found that a dodeca-nucleosome in the two-helix zigzag conformation breaks into structures with nucleosome clutches and a mix of trimers and tetramers under tension. Such unfolded configurations can also be stabilized through trans interactions with other chromatin chains. Our study suggests that unfolding from chromatin fibers could contribute to the irregularity of in vivo chromatin configurations. We further revealed that chromatin segments with fibril or clutch structures engaged in distinct binding modes and discussed the implications of these inter-chain interactions for a potential sol–gel phase transition.     

Changes in Raman vibrational bands of calf thymus DNA during the B-to-A transition

The B -to-A conformational transition of calf thymus DNA fibers was followed employing Raman spectroscopy. The transition was induced by soaking DNA fibers in water/ethanol mixtures increasing from 60 to 85% ethanol (v/v). Intensity changes of 17 Raman vibrational bands were quantified in the region from 400 to 860 cm^?1. Two bands at 500 and 784 cm^?1 were employed as internal standards. These bands do not appear to change in intensity with ethanol concentration. Large intensity changes relative to these two bands are observed between 70 and 74% ethanol for backbone vibrations at 708, 808, and 835 cm^?1, and base vibrations at 682, 730, and 750 cm^?1. These results indicate that a highly cooperative conformational change takes place between different portions of DNA in the B -to-A transition. Relative intensity changes preceding the onset of the major transition are observed in only two bands; at 835 cm^?1, assigned to a ribose–phosphate vibration, and at 750 cm^?1, assigned to thymine. The implications of these pretransition changes are discussed.     

Fine structure of the fertilization membranes of sea urchin embryos

The fine structure of the fertilization membranes from S. purpuratus embryos has been studied with the electron microscope. Isolated membranes before and after their full development and membranes formed under the influence of 10⁻³% cystine have been observed. The membrane structure was found to be trilamella: a middle layer about 200 Å thick, which originally was the vitelline membrane, and about 175 Å thick peripheral layers organized by the “crystalline material” from the cortical granules. These surface layers were again found to be trilaminated structure composed of a monolayer of parallel, closely packed flat fibrils, about 160 Å wide and 75 Å thick, adhering on both sides to parallel, 40–50 Å thick filaments separated from each other by about 100 Å and intersecting with the fibrils by an angle of about 75 °.     

Structure of the 300A chromatin filament: X-ray diffraction from oriented samples

X-ray diffraction patterns have been obtained from partially oriented samples of 300A chromatin filaments. The chromatin was prepared by methods that preserve its structure, and conditions were found in which the 300A filaments spontaneously form ordered aggregates, so that it was not necessary to pull fibers. The diffraction patterns show a meridional band at 110A, and equatorial bands at 340, 57, 37, and 27A. These patterns, together with patterns calculated from the known 7A electron density map of the nucleosome core particle, imply side-to-side packing of nucleosomes in the direction of the 300A filament, and radial packing around it. These results are consistent with the "solenoid" model of Finch and Klug, and are inconsistent with many other proposed models.     

A functional fragment of Tau forms fibers without the need for an intermolecular cysteine bridge

We study the aggregation of a fragment of the neuronal protein Tau that contains part of the proline rich domain and of the microtubule binding repeats. When incubated at 37 °C with heparin, the fragment readily forms fibers as witnessed by Thioflavin T fluorescence. Electron microscopy and NMR spectroscopy show bundled ribbon like structures with most residues rigidly incorporated in the fibril. Without its cysteines, this fragment still forms fibers of a similar morphology, but with lesser Thioflavin T binding sites and more mobility for the C-terminal residues.     

Formation of amyloid fibrils via longitudinal growth of oligomers

Mature amyloid fibrils are believed to be formed by the lateral association of discrete structural units designated as protofibrils, but this lateral association of protofibrils has never been directly observed. We have recently characterized a thioesterase from Alcaligenes faecalis, which was shown to exist as homomeric oligomers with an average diameter of 21.6 nm consisting of 22 kDa subunits in predominantly beta-sheet structure. In this study, we have shown that upon incubation in a 75% ethanol solution, the oligomeric particles of protein were transformed into amyloid-like fibrils. TEM pictures obtained at various stages during fibril growth helped us to understand to a certain extent the early events in the fibrillization process. When incubated in 75% ethanol, oligomeric particles of protein grew to approximately 35-40 nm in diameter before fusion. Fusion of two oligomers of 35-40 nm resulted in the formation of a fibril. Fibril formation was accompanied by a reduction in the diameter of the particle to approximately 20-25 nm along with concomitant elongation to approximately 110 nm, indicating reorganization and strengthening of the structure. The elongation process continued by sequential addition of oligomeric units to give fibers 500-1000 nm in length with a further reduction in diameter to 17-20 nm. Further elongation resulted in the formation of fibers that were more than 4000 nm in length; the diameter, however, remained constant at 17-20 nm. These data clearly show that the mature fibrils have assembled via longitudinal growth of oligomers and not via lateral association of protofibrils.     

An actin-like protein from amoebae of dictyostelium discoideum

An actin-like protein has been isolated and purified from amoebae of Dictyostelium discoideum. The 3.7S protein polymerizes upon addition of 0.1 m KCl to a polymer of 26S. An increase in viscosity accompanies this polymerization and electron micrographs have revealed beaded, helical filaments with a diameter of 60–75 Å and an axial periodicity of 350 Å. These F-actin-like filaments produced a 5-fold activation of muscle myosin Mg-ATPase at low ionic strength. When incubated with rabbit muscle heavy meromyosin (HMM) the amoeba F-actin-like protein formed typical “arrowhead” structures with polarized binding of HMM and arrowhead spacings of 350 Å. In SDS polyacrylamide disc gel electrophoresis the purified amoeba protein migrates as a single band corresponding to a molecular weight of 48,000 daltons. The amino acid composition is very similar to that of muscle actin and includes the unusual amino acid 3-methylhistidine.     

Thermodynamic studies of the assembly in vitro of native collagen fibrils

Measurements of the solubility of calf-skin tropocollagen in neutral phosphate buffers in the temperature range 20-37 degrees C show that native collagen fibril formation is an endothermic process made thermodynamically favourable by a large positive entropy of precipitation associated with structural changes in the surrounding solvent. The effect of inorganic ions and small solute molecules on precipitation seems to be correlated with their structural effects on liquid water. Heterogeneity in the precipitation properties of the collagen solutions may be related to changes in the configurational entropy of the macromolecules due to intramolecular cross-linking.     

Spermiogenesis and chromatin condensation in the common tree shrew, <Emphasis Type="Italic">Tupaia glis</Emphasis>

We have investigated the cellular characteristics, especially chromatin condensation and the basic nuclear protein profile, during spermiogenesis in the common tree shrew, Tupaia glis. Spermatids could be classified into Golgi phase, cap phase, acrosome phase, and maturation phase. During the Golgi phase, chromatin was composed of 10-nm and 30-nm fibers with few 50-nm to 60-nm knobby fibers. The latter were then transformed into 70-nm knobby fibers during the cap phase. In the acrosome phase, all fibers were packed into the highest-order knobby fibers, each about 80–100 nm in width. These chromatin fibers became tightly packed in the maturation phase. In a mature spermatozoon, the discoid-shaped head was occupied by the acrosome and completely condensed chromatin. H3, the core histone, was detected by immunostaining in all nuclei of germ cell stages, except in spermatid steps 15–16 and spermatozoa. Protamine, the basic nuclear protein causing the tight packing of sperm chromatin, was detected by immunofluorescence in the nuclei of spermatids at steps 12–16 and spermatozoa. Cross-immunoreactivity of T. glis H3 and protamine to those of primates suggests the evolutionary resemblance of these nuclear basic proteins in primate germ cells. This work was supported by the Thailand Research Fund (Senior Research Fellowship to Prof. Prasert Sobhon).     

Chromatin condensation and acrosome development during spermiogenesis of Ensis ensis (Mollusca,Bivalvia)

We describe chromatin condensation and acrosome development during spermiogenesis of Ensis ensis. The overall shape of the mature spermatozoon corresponds to the primitive type. The nucleus is oval and on its superior pole there is an elongated acrosome; the middle piece contains four mitochondria around the centriolar complex. The condensation of the nuclei seems to occur in three steps: first the diameter of chromatin fibers increases slightly from 17 to 20 nm; second, in midspermatids fiber pairs coalesce; and third, the coalescence continues by addition of other fibers until the nuclei become highly compacted. Chromatin changes are related with nuclear protein composition. Small proacrosomal vesicles show two regions of different electron density. At a later stage they fuse to give a single, spherical vesicle in round spermatids, which migrates to the upper pole and transforms into a tapered acrosome (18 μm long) with a central channel filled with finely fibrous material. © 1994 Wiley-Liss, Inc.     

Structural Analysis of Human Lysozyme Using Molecular Dynamics Simulations

Abstract

In this study, various molecular dynamics simulations were conducted to investigate the effects of ethanol and temperature on the conformational changes of human lysozyme, which may lead insights into amyloidosis. The analyses of some important structural characteristics, such as backbone root-mean-square deviation, secondary structural stability, radius of gyration, accessible surface area, and hydrophobic contact of the hydrophobic core all show that ethanol tends to destabilize human lysozyme at high temperatures. It can be attributed to that higher temperatures result in the destruction of the native structure of this protein, leading to the exposure of the interior hydrophobic core. At this stage, ethanol plays a role to destroy this region by forming hydrophobic interactions between protein and solvent due to its lower polarity comparing to water. Such newly formed intermolecular interactions accelerate the unfolding of this protein, starting from the core between the a- and β-domains. Our results are in good agreement with the previous hypothesis suggesting that the distortion of the hydrophobic core at the α- and β-interface putatively results in the formation of the initial “seed” for amyloid fibril. Although the present results cannot directly be linked to fibril formation, they still provide valuable insights into amyloidosis of human lysozyme.